Species is already checked during trimming step
In “sample_sheet.tsv”" (input for alignment-nf), there may be multiple replicate libraries (“id”) for the same strain (“strain”). Here will output stats for all replicates combined.
Output stats_strain_all.tsv contains stats for all strains, with all replicates combined.
Output stats_strains_with_low_values.tsv contains strains with:
Output sample_sheet_for_seq_sheet.tsv is formatted to be put on to Google sequencing sheet, which contains a column of coverage.
## [1] "strains with too few reads (< 10000): "
If a strain had most reads mapped (> 90%, indicating correct species), and coverage is a bit low (between 10x ~ 15x), probably still worth keeping for variant calling.
## [1] "low reads input: 0 strains"
## [1] "low percent reads mapped: 0 strains"
## [1] "low average coverage: 14 strains"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)
##
## Matrix products: default
## BLAS: /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
## LAPACK: /hpc/software/R/3.6.0/lib64/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] plotly_4.9.2 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.4
## [5] purrr_0.3.3 readr_1.3.1 tidyr_1.0.2 tibble_2.1.3
## [9] ggplot2_3.2.1 tidyverse_1.3.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.6 lubridate_1.7.4 lattice_0.20-38 assertthat_0.2.1
## [5] digest_0.6.24 mime_0.9 R6_2.4.1 cellranger_1.1.0
## [9] backports_1.1.5 reprex_0.3.0 evaluate_0.14 httr_1.4.1
## [13] pillar_1.4.3 rlang_0.4.4 lazyeval_0.2.2 readxl_1.3.1
## [17] rstudioapi_0.11 data.table_1.12.8 DT_0.12 rmarkdown_2.1
## [21] labeling_0.3 htmlwidgets_1.5.1 munsell_0.5.0 shiny_1.4.0
## [25] broom_0.5.4 compiler_3.6.0 httpuv_1.5.2 modelr_0.1.5
## [29] xfun_0.12 pkgconfig_2.0.3 htmltools_0.4.0 tidyselect_1.0.0
## [33] fansi_0.4.1 viridisLite_0.3.0 crayon_1.3.4 dbplyr_1.4.2
## [37] withr_2.1.2 later_1.0.0 grid_3.6.0 xtable_1.8-4
## [41] nlme_3.1-139 jsonlite_1.6.1 gtable_0.3.0 lifecycle_0.1.0
## [45] DBI_1.1.0 magrittr_1.5 scales_1.1.0 cli_2.0.1
## [49] stringi_1.4.6 farver_2.0.3 fs_1.3.1 promises_1.1.0
## [53] xml2_1.2.2 generics_0.0.2 vctrs_0.2.2 tools_3.6.0
## [57] glue_1.3.1 hms_0.5.3 crosstalk_1.0.0 fastmap_1.0.1
## [61] yaml_2.2.1 colorspace_1.4-1 rvest_0.3.5 knitr_1.28
## [65] haven_2.2.0